There should be no difference at all on a CTP device. We have switched between negative and positive a number of times (Kodak 830N, Trillian, Elekta XD, Sonora, Sonora X and a few other variants in between) we have not experienced any variation at he press. In the days of film, negative plates had a slight dot gain during exposure while positive plates had a slight decrease in dot size, this was due to light leaking under the opaque parts of the film on the vacuum frame, as CTP plates are imaged direct, this is no longer an issue.
